Thermo Fisher Scientific GeneChip™ System 3000Dx v.2 User guide

UserGuide

For In Vitro Diagnostic Use.

IVD

REF

GeneChip® System 3000Dx v.2

Instrument Operation and Use

703227 Rev. 2

2

IVD

Trademarks

Affymetrix®, CytoScan®, and GeneChip® are registered trademarks of Affymetrix, Inc. All other trademarks are the property of their

respective owners.

Patents

Autoloaders: Products may be covered by one or more of the following patents: U.S. Patent Nos. 6,511,277; 6,604,902; 7,108,472; 7,871,812

and other U.S. and foreign patents.

Fluidics Stations: Products may be covered by one or more of the following patents: U.S. Patent Nos. 6,114,122; 6,391,623; 6,422,249;

6,715,500 and other U.S. and foreign patents.

Scanners: Products may be covered by one or more of the following patents: U.S. Patent Nos. 5,981,956; 6,171,793; 6,207,960; 6,225,625;

6,490,533; 6,511,277; 6,604,902; 6,650,411; 6,643,015; 6,741,344; 6,789,040; 6,813,567; 7,062,092; 7,108,472; 7,130,458; 7,222,025; 7,406,391;

7,689,022; 7,983,467; 7,992,098; 8,208,710; 8,233,735; 8,391,582 and other U.S. and foreign patents.

Array Software: Products may be covered by one or more of the following patents: U.S. Patent Nos. 5,733,729; 5,795,716; 6,066,454;

6,090,555; 6,185,561; 6,188,783; 6,223,127; 6,228,593; 6,229,911; 6,308,170; 6,361,937; 6,420,108; 6,484,183; 6,505,125; 6,510,391; 6,532,462;

6,546,340; 6,567,540; 6,584,410; 6,611,767; 6,687,692; 6,826,296; 6,882,742; 6,957,149; 6,965,704; 6,996,475; 7,068,830; 7,130,458; 7,215,804;

7,424,368; 7,634,363; 7,822,555; 7,991,564; 7,992,098; 8,190,373; 8,498,825 and other U.S. and foreign patents.

Manufacturer

Copyright

Affymetrix Inc.

3450 Central Expressway

Santa Clara, CA 95051 USA

Contents

IVD

Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Indications for Use . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Instrument Usage Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Other Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Context-Sensitive Help . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

Complete Help System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

Terminology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

Text Alerts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

Technical Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

European Representative . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

Chapter 2 System Overview. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Standard Hardware Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Optional Hardware Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

Optional Hybridization Oven . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

AMDS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

ASM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Workflow Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

Administrator Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

User and System Information Panes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

Chapter 3 System Operation Basics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Start the Workstation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Log onto AMDS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Start the GeneChip® Fluidics Station 450Dx v.2 and Scanner 3000Dx v.2 . . . . . . . . . . . . . . 19

Log Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Shut Down . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Contiguous Select and Enter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Non-Contiguous Select and Enter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

Chapter 4 GeneChip® Fluidics Station FS450Dx v.2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

Components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

Assay Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

Barcode Reader Usage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

Fluidics Station 450Dx v.2 Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

Fluidics Station Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Start Fluidics Station . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Prime Fluidics Station . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

Run a Fluidics Station Protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31

Contents 4

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Shut Down Fluidics Station . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

Instrument Care . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

Bleach Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36

Rinse Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Set Peristaltic Tubing Maintenance Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

Replace Peristaltic Tubing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

Troubleshooting Decision Tree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

Problems and Solutions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45

Other Problems and Solutions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

When to Contact Affymetrix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

Chapter 5 GeneChip® Scanner 3000Dx v.2 with AutoLoaderDx v.2 . . . . . . . . . . . . . . . . . 51

Precautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

Laser Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

Electrical Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

Workstation-AutoLoaderDx v.2 Connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

Scanner Indicator Lights and On/Off Button . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57

Use of Tough-Spots™ to Prevent Leaks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

Load Arrays into Carousel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

Start Scanner . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61

Shut Down Scanner . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61

Disable the AutoLoaderDx v.2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61

Scanner Troubleshooting Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63

Scanner Operation Issues Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63

Scanner Diagnostic Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64

Scanner Error Messages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

Manual Removal of Lodged Array Cartridge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66

When to Contact Affymetrix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68

Appendix A Specifications and Regulatory Information . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

GeneChip® Fluidics Station 450Dx v.2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

Scanner . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

Quick Reference Card . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70

Regulatory Compliance–GeneChip® Fluidics Station 450Dx v.2 . . . . . . . . . . . . . . . . . . . . . . . . 72

Regulatory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72

China RoHS Restriction of Hazardous Substances Compliance . . . . . . . . . . . . . . . . . . . . . . . 73

Regulatory Compliance–GeneChip® Scanner 3000Dx v.2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76

Regulatory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78

Chapter 1

IVD

Introduction

This User Guide gives an overview of the system operation of the GeneChip® System 3000Dx v.2 (GCS

3000Dx v.2) and detailed information for use of the instrument components.

In this chapter:

Indications for Use

Instrument Usage Information

Other Documentation

Context-Sensitive Help

Complete Help System

Terminology

Text Alerts

Technical Support

European Representative

Indications for Use

GCS 3000Dx v.2 is intended to measure fluorescence signals of labeled DNA and RNA targets

hybridized to Affymetrix arrays.

Instrument Usage Information

The expected life of the GCS 3000Dx v.2 system is at least 8 years, provided the system is used and

maintained according to manufacturer’s recommendations. For optimal operational performance, please

follow recommended maintenance and service schedules and permit only qualified service personnel to

replace parts when required.

Other Documentation

Affymetrix® Molecular Diagnostic Software (AMDS) User Guide

Affymetrix® Molecular Diagnostic Software (AMDS) Quick Reference Card

Tooltip help1

Online Help2

Context-Sensitive Help

The Affymetrix® Molecular Diagnostic Software (AMDS) is the operating software for the GCS 3000Dx

v.2. The AMDS online help system provides content-sensitive help.

1. Click Help.

2. Use the question mark cursor to click on parts of the window.

The help topic associated with the selected area is shown in the lower half of the center panel and

includes information about the:

Workflow Pane

Administrator Pane

1To use this feature, place mouse cursor over an interface component to view its description or un-truncate truncated data.

2To access, click:

Chapter 1 | Introduction 6

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User Details Pane

Device Status Pane

Alerts and Alert Details Panes

Complete Help System

To view:

1. Click Help

2. Click anywhere on the AMDS interface.

3. On the Help toolbar, click Show Navigation (Figure 1.1) to see the complete help system.

4. Use the navigation buttons to search for and select help topics.

Terminology

Test Request—Unique record of an assay performed on a specimen. Repeated runs of the same

specimen are represented by multiple test requests. Each test request is associated with a specific array

cartridge.

Assay Software Module (ASM)—The software package that runs an assay. ASMs are supplied by

Affymetrix or authorized partners in the form of a CD.

Assay—Procedure that processes the specimen to produce a result, includes bench work and running

through the GCS3000Dx v2 workflow. In this manual, assay refers to the ASM.

Array—A microarray is a glass substrate with oligonucleotide probes. A plastic cartridge surrounds and

protects the array and forms the array cartridge. Array also typically refers to the array cartridge.

Fluidics station or FS450Dx–GeneChip® Fluidics Station 450Dx v.2.

Scanner–GeneChip® Scanner 3000Dx v.2 with AutoLoaderDx v.2.

Text Alerts

Text alerts draw your attention to a particular piece of information. There are five types of text alerts:

Note, Important, Caution, Warning, and Danger.

Figure 1.1 Show Navigation Button on Help tool bar

NOTE: Information that may be of interest or of help to a user but is not critical to the primary

purpose of the text.

IMPORTANT: Information that is essential to the successful use of a product or the

completion of a procedure and is not safety related.

CAUTION: An alert to the user of hazards that, if not avoided, can cause minor or moderate

personal bodily injury and/or damage to an instrument or loss of data.

WARNING: Alerts the user to hazards that, if not avoided, can cause serious bodily injury or

death, or produce potentially incorrect data that could cause harm to a patient.

DANGER: Dangers alert the user to an imminent hazard that, if not avoided, will cause

serious bodily injury or death, or will produce a result that could cause serious harm to a

patient.

Chapter 1 | Introduction 7

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Technical Support

Consult this user manual and online help and review the troubleshooting sections before you contact

Affymetrix technical support for unresolved issues.

For problems with the fluidics station or scanner, especially under any of the following conditions, unplug

the instrument from the power source and contact Affymetrix technical support.

Power cord is damaged or frayed

The instrument does not perform to the specifications in Table 4.5 on page 49 after service or

calibration.

For complete contact information and specific regional support contact information, go to

www.affymetrix.com/browse/contactUs.jsp. Have the model and serial number available when you call

technical support.

.

European Representative

Emergo Europe

Molenstraat 15

2513 BH, The Hague

The Netherlands

Affymetrix, Inc.

3450 Central Expressway

Santa Clara, CA 95051

USA

www.thermofisher.com

Email: [email protected]

Tel: 1-800-955-6288

Chapter 2

IVD

System Overview

The GeneChip® System 3000Dx v.2 (GCS 3000Dx v.2) consists of hardware and software components

for processing microarrays based on assay parameters. The Affymetrix Molecular Diagnostic Software

(AMDS) manages assay workflows.

In this chapter:

Hardware

Software

AMDS User Interface

Hardware

Standard Hardware Components

The GCS 3000Dx v.2 comes with these standard hardware components:

System Workstation

GeneChip® Fluidics Station 450Dx v.2 (fluidics station)

GeneChip® Scanner 3000Dx v.2 (scanner) with AutoLoaderDx v.2

Barcode Reader

Hardware Firewall

System Workstation, Monitor, and Soundbar

AMDS is loaded on the workstation (Figure 2.1). It provides the hardware interface to other system

components. Because the workstation is a dedicated system, it is locked down to prevent other uses. A

monitor and soundbar (not pictured) are part of the workstation system.

Figure 2.1 System Workstation

Chapter 2 | System Overview 10

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Fluidics Station 450Dx v.2

The Fluidics Station 450Dx v.2 (Figure 2.2) consists of four modules installed in a single housing. Each

module holds a single array and performs the hybridization, washing, and staining functions for that

array. Up to eight stations can communicate with one system workstation.

Each module controls the addition of target and staining fluids to the array cartridge and array washing.

Each module contains a pump, valve, thermo-electric system, and LCD that are controlled by scripts

provided in the Assay Software Module (ASM). These scripts are automatically downloaded to each

module and stored in its electronic memory.

Figure 2.2 Fluidics Station 450Dx v.2

Chapter 2 | System Overview 11

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Scanner 3000Dx v.2 with AutoLoaderDx v.2

The Scanner 3000Dx v.2 with AutoLoaderDx v.2 (Figure 2.3) is a wide-field, epifluorescent, confocal,

scanning laser microscope. It scans the chip after staining on the Fluidics Station 450Dx v.2. Array

cartridges are loaded into the scanner by the AutoLoaderDx v.2 (an automatic handler) before scanning

and returned to the AutoLoaderDx v.2 when scanning finishes.

Barcode Reader

The barcode reader (Figure 2.4) is used to enter barcode-encoded information from:

Array cartridge

Fluidics station

Specimen identification

Reagent lot number

Other identification information

Figure 2.3 Scanner 3000Dx v.2 with

AutoLoaderDx v.2

Figure 2.4 Barcode Reader

Chapter 2 | System Overview 12

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Hardware Firewall

The hardware firewall (Figure 2.5) protects against unauthorized access to the workstation. It is a

required component of the system.

Optional Hardware Components

Additional components are:

Uninterruptible power supply (UPS)

Printer

Contact Affymetrix for optional hardware requirements.

Optional Hybridization Oven

Depending on the type of assay, you may need a hybridization oven to prepare arrays for testing.

Requirements for a hybridization oven that connects to AMDS are:

Requirements for a hybridization oven that does not connect to AMDS are:

Figure 2.5 Hardware Firewall

Input Voltage 100–120 VAC, 5 A maximum or 220–240 VAC, 2.5 A maximum

50–60 Hz

Rotisserie Rotation Speed 10–80 RPM, programmable to 1 RPM

Oven Temperature Set Point

Programmable Range

30–70 °C, programmable to 0.1°C

Time to Temperature 30 minutes from ambient to 60°C

Oven Temperature Accuracy ±1.0°C from 35–60°C

Communications Nine-pin RS-232 port, 9600 Baud rate

Monitors and reports oven temperature, rotisserie rotation rate, and oven

status

Input Voltage 100–120 VAC, 5 A maximum or 220–240 VAC, 2.5 A maximum

50–60 Hz

Chapter 2 | System Overview 13

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Software

There are two types of software:

Affymetrix® Molecular Diagnostic Software (AMDS)

Assay Software Modules (ASM)

AMDS

AMDS is the user interface for the system. It provides control of the instruments, assay workflow, and

the data collection and management processes. When array scanning finishes, data is passed through

AMDS to the ASM. Alternatively, AMDS transfers the data to a network location for downstream

analysis. AMDS also assists you in installing and deactivating an ASM.

AMDS tools:

Control assay workflows and show test results

Perform administrative functions

Troubleshoot the system

ASM

ASMs provide the necessary parameters for processing an array through its entire workflow. ASMs

contain the algorithms and reporting functions to produce the clinical result specific to that ASM. ASM

user manuals give detailed instructions that are unique to specific assays.

AMDS User Interface

The AMDS user interface consists of three sections (Figure 2.6):

Left Panel–Workflow and Administration panes

Center Panel–Gives information based on your selection in the left pane; also shows online help when

selected

Right Panel–User Details, Device Status, Alert, and Alert Details panes

Rotisserie Rotation Speed 10–80 RPM, programmable to 1 RPM

Oven Temperature Set Point

Programmable Range

30–70°C, programmable to 0.1°C

Time to Temperature 30 minutes from ambient to 60°C

Oven Temperature Accuracy ±1.0°C from 35–60°C

Communications NA

NOTE: For ASMs that allow auto-transfer of data, AMDS auto-transfers data (including DAT

and CEL files) to your network where it is available for downstream analysis. Your network

location must have ample storage and the correct access permissions for this auto-transfer

feature to work.

Chapter 2 | System Overview 14

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Workflow Pane

Buttons are:

Active Worklist

Registration

Hybridization Oven

Fluidics

Scanner

Non-Active Worklist

When you select an item, the associated worklist opens in the center panel. A blue arrow next to the

selected item shows that it has been selected.

Active Worklist

A test request is active until processing finishes or it is canceled. While a test request is active, you can

view its status by clicking Active Worklist. Data associated with a test request appear only on the Active

Worklist and the current workflow stage of the test request. Active Worklist enables you to:

View the current status of all active test requests

Create new test requests

View and approve test results

You cannot edit information in the Active Worklist. This worklist is maintained and updated by AMDS.

Figure 2.6 AMDS User Interface

Right Panel

Left Panel

Center Panel

Chapter 2 | System Overview 15

IVD

Registration Worklist

The Registration Worklist is the next step in the workflow. This step allows you to associate a test request

with an array cartridge and adds the target preparation reagent kit lot numbers (if these are supported by

the ASM).

Hybridization Oven Worklist

The Hybridization Worklist step allows you to enter oven hybridization data and processes the array in

the hybridization oven.

Some assays do not use a hybridization oven. Instead, they perform hybridization on the fluidics station.

Test requests that are associated with these assays skip this step and proceed to fluidics.

Fluidics Worklist

The Fluidics step allows you to associate a test request with a fluidics station and module and runs the

associated fluidics script. The selected station and module wash and stain the array.

Scanner Worklist

The Scanner selection opens the Scanner Worklist. AMDS automates control of the scanner and uses

the assay information provided by the ASM to manage the scanner settings for each type of array. After

scanning, AMDS automatically grids the image, computes intensities, and either runs an ASM-specific

analysis algorithm to generate a result or transfers the files to data storage.

Non-Active Worklist

The Non-Active Worklist selection shows non-active test requests. The system moves test requests to

the Non-Active Worklist when processing in AMDS finishes.

Administrator Pane

The Administrator Pane (Figure 2.7) is below the Workflow Pane. It is visible to everyone, but only

Laboratory Supervisors and System Maintainers use it.

User and System Information Panes

The right panel of the user interface has four panes that give up-to-date user details and device status.

User Details Pane

The User Details pane (Figure 2.8) is in the top portion of the right panel. Here you can:

Log off

See who is logged in and their role

See system time and date

Change passwords

Figure 2.7 The

Administrator Pane

Chapter 2 | System Overview 16

IVD

Shut down the system

Device Status Pane

The Device Status pane is just below the User Details pane (Figure 2.9).

This pane is an instrument status dashboard, providing color-coded status for each system device.

Green–Device is operating normally

Yellow–Abnormal condition detected

Red–Communications issue or a device failure

AMDS provides status for the fluidics station, scanner, and printer, and for hybridization oven, only if

connected.

Figure 2.8 User Details Pane

Figure 2.9 Device Status Pane

Chapter 2 | System Overview 17

IVD

Alert and Alert Details Panes

The Alert pane (Figure 2.10) provides alerts if a component or process is not operating as expected.

When you click on an alert in this pane, information about the alert is shown in the Alert Details pane

(Figure 2.11).

Alert information may contain:

Specimen ID

Assay Name

Workflow Step

Date/Time

Alert Details

Recommended resolution

Figure 2.10 Alerts panes

Figure 2.11 Alerts Details panes

Chapter 3

IVD

System Operation Basics

In this chapter:

Before you Begin

Start and Shut Down the System

Change Password

Using the Barcode Reader

Edit Multiple Fields in AMDS

How to Hold Array Cartridges

E-Signatures

Before you Begin

Read this entire manual and familiarize yourself with the instrument, software, and procedure.

Start and Shut Down the System

Start the Workstation

Turn on the computer workstation to launch the Affymetrix® Molecular Diagnostic Software (AMDS).

AMDS performs:

A system self-test to confirm the operational status of the system and ensure that all components are

connected and operating correctly

Housekeeping tasks to ensure that all test requests are in known states and can be processed

When AMDS completes the self-test, the AMDS User Logon window opens.

Log onto AMDS

1. Obtain your User Name and Password from your Affymetrix service engineer or your system

administrator.

2. Login (Figure 3.1):

A. Enter your User Name.

B. Enter your Password.

Chapter 3 | System Operation Basics 19

IVD

C. Click Log On.

AMDS authenticates your credentials and provides functionality based on your user role.

Start the GeneChip® Fluidics Station 450Dx v.2 and Scanner 3000Dx v.2

When your test requests have reached the associated worklists, turn on the fluidics station and scanner.

Scanner laser takes about 10 minutes to warm up.

Log Off

Logging off does not terminate the active workflow processes. If there are test requests in hybridization,

fluidics or scanning, AMDS continues to process them.

1. Go to User Details pane (Figure 3.2)

2. Click Log Off.

Figure 3.1 AMDS User Log On

WARNING: Laser in use during scanning.

IMPORTANT: To preserve the lifetime of the scanner laser, turn off the scanner when it is not

in use for an extended period of time, such as overnight or a weekend.

CAUTION: AutoLoaderDx v.2 carousel is in motion during start-up sequence.

Figure 3.2 The User Details Pane

Chapter 3 | System Operation Basics 20

IVD

Shut Down

1. Go to User Details pane.

2. Click Shut Down.

3. Turn off instrumentation.

Change Password

1. Go to User Details pane.

2. Click Change Password.

3. In the Change Password dialog box, enter your old password Appendix 3.

4. Enter and confirm your new password.

5. Click OK.

Using the Barcode Reader

Use the barcode reader to:

Enter a Specimen ID for a test request

Associate a test request with an Array ID

Associate a test request with reagent lot numbers

Associate an array with a fluidics station and module

Edit Multiple Fields in AMDS

Contiguous Select and Enter

1. Click on first row of your selection.

2. Press and hold Shift key.

3. Click on last row of your selection.

4. Press and hold Ctrl key and:

Select from drop-down in last row

IMPORTANT: If there are test requests in progress, a confirmation dialog box opens. Click Yes

to initiate an orderly shutdown of the system. All tests requests that are “In Progress” go into

an error state and must be re-run.

Figure 3.3 Change Password

Chapter 3 | System Operation Basics 21

IVD

or

Click in field in last row and scan barcode

or

Click in field in the last row, release the Ctrl key, and enter value

5. Click outside of field.

Non-Contiguous Select and Enter

1. Click on first row of your selection.

2. Press and hold Ctrl key.

3. Individually select each row.

4. While holding Ctrl key:

Select from drop-down in last row

or

Click in field in last row and scan barcode

or

Click in field in last row, release Ctrl key, and enter value

5. Click outside of field.

How to Hold Array Cartridges

Arrays come mounted in a plastic package to form an array cartridge (Figure 3.4). The array contains

oligonucleotide probes on the inner glass surface. A chamber in the plastic package directly under the

chip acts as a reservoir where hybridization and washing and staining occur.

Although the inner glass surface is protected, any contamination or scratches on the outer surface of the

glass can compromise the integrity of the scan.

Figure 3.4 Example: CytoScan Dx Array Cartridge

IMPORTANT: Do not touch the surface of the glass with your fingers. Skin oils and other

substances, such as lotions or ink, can fluoresce. If the array surface is dirty, carefully clean it

with a nonabrasive laboratory tissue.

Plastic cartridge

Front

Notch

Back

Septa

Probe array on

glass substrate

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Thermo Fisher Scientific GeneChip™ System 3000Dx v.2 User guide

Thermo Fisher Scientific GeneChip™ System 3000Dx v.2 User guide

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Thermo Fisher Scientific GeneChip&trade; System 3000Dx v.2 User guide

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Thermo Fisher Scientific GeneChip™ System 3000Dx v.2 User guide

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